Banks and mortgage companies thought that they were getting a clear set of ground rules earlier this month when regulators spelled out long-awaited rules clarifying how they could satisfy new mortgage standards. But a new court ruling is calling all of that clarity into question.

The Consumer Financial Protection Bureau issued the “qualified mortgage” definition three weeks ago, which told banks how they could reduce their legal liability under new rules that require them to ensure borrowers have the ability to repay a mortgage. (Here’s a look at what those rules mean for banks and consumers.)

Now, the authority of the CFPB’s director, Richard Cordray, is in doubt because he was appointed by President Barack Obama without Senate confirmation during the Senate’s recess early last year.

A federal appeals court ruled on Friday that the president’s recess appointments to the National Labor Relations Board—which were made at the same time as Mr. Cordray’s appointment—were unconstitutional. Though the case doesn’t directly address the legitimacy of Mr. Cordray’s appointment, the coordinated timing of the two greatly raises the prospect that the court would rule the same way in a similar suit challenging Mr. Cordray’s authority.

So what does all of this mean for banks and mortgage lenders? In Friday’s decision regarding the NLRB appointments, a soda bottler and distributor challenged an adverse ruling in a union dispute, saying the NLRB didn’t have authority because the recess appointments weren’t valid, leaving the agency without a quorum or the authority to conduct business. The three-judge panel of the U.S. Court of Appeals for the District of Columbia Circuit agreed. Because the NLRB appointments weren’t valid, neither was their order.

Over at the CFPB, the implications could fall along the same lines: the QM rule that was issued on Jan. 10 might not be enforceable, were it challenged in court, if Mr. Cordray’s appointment was deemed invalid.

So does this mean banks may not have to follow the qualified mortgage rule issued by the CFPB? Not so fast. Here’s where things get really messy: the Dodd-Frank Act, which gave the CFPB’s director the authority to flesh out the “qualified mortgage” definition, also provides an alternate definition that was to take effect on Jan. 21 if the CFPB hadn’t exercised its authority to issue its own rule.

So if the CFPB’s 804-page rule isn’t valid, then the alternate definition spelled out in the Dodd-Frank law could kick in.

Until courts clarify the validity of Mr. Cordray’s appointment—and the rules that the CFPB just issued—banks face the prospect of having two different “qualified mortgage” rules: the 804-pager issued on Jan. 10 that takes effect next year (and which banks generally liked), and the alternate definition spelled out in the Dodd-Frank Act, which was to take effect on Jan. 21 of this year (and which would be much stricter for lenders).

It’s likely that it will take some time for all of this to get sorted out. The NLRB decision could get appealed to the Supreme Court, and the Treasury Department could intervene and say that it had authority, in the absence of a fully-empowered CFPB, to finalize the ability-to-repay rules.

But the clarity that lenders say they’re coveting may have to wait for the courts to weigh in.